Abstract
Aim: We conducted an in silico study on Urolithin and different antimicrobial agents targeting virus protease and peptidase.
 Methodology: The docking study was completed by using docking tools. Drug compounds and COVID-19 receptor molecules were prepared, docking was performed and interaction was visualized through Discovery Studio visualizer.
 Results: Urolithin A has interacted against peptidase (PDB ID:2GTB) with binding energy -6.93 kcal/mol and against protease (PDB ID:6LU7) with the binding energy -5.46 kcal/mol, while Urolithin B has interacted to peptidase (PDB ID:2GTB) with binding energy -6.74 kcal/mol and with protease it interacted with a binding energy -4.67 kcal/mol. The antimicrobial agent Ofloxacin was found to interact against protease (PDB ID:6LU7) with a binding energy -6.84 kcal/mol and against protease (PDB:6LU7) with a binding energy -8.00 kcal/mol.
 Conclusion: The most common interacting amino acids of target enzymes of the virus with studied drugs were His41, His164, Met165, Glu166, Gln189. From the docking studies, it is observed that Ofloxacin and Urolithin have the potential to inhibit the virus protease as well as peptidase significantly and these could prevent the entry of the virus to the inside of the host cell. Thus, further antiviral research on these antimicrobial agents and Urolithin could be helpful to control the COVID-19 disease.
Highlights
The pathogenic human to human transmitted, respiratory illness caused by virus SARS-CoV-2
Sulfamethoxazole has interacted with enzyme peptidase (PDB ID:2GTB) with binding energy 7.01 kcal/mol, inhibition constant 15.20 uM and among five hydrogen bonds two were A:GLY143:HN - :UNK1:O9, A:SER144:HG :UNK1:O10 formed at a distance 2.5023 and 2.35075 Å respectively
Ofloxacin was analyzed to interact against the virus target (PDB ID:6LU7) with a binding energy -8.00 kcal/mol, inhibition constant 17.02 uM and six involved hydrogen bonds were A:HIS41:HE2 - :UNK1:O11, A:GLY143:HN :UNK1:O25, A:CYS145:HN - :UNK1:O26, A:GLU166:HN - :UNK1:O4, UNK1:H46 A:LEU141:O, UNK1:C22 - A:THR190:O form at a distance 2.9611, 1.83274, 2.57688, 1.94514, 1.789, 2.9369, The amino acids residues involved in hydrophobic interactions were His41, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Gln189, Thr190, Gln192
Summary
The pathogenic human to human transmitted, respiratory illness caused by virus SARS-CoV-2. It was appeared at the end of December 2019 in Wuhan city of China and become pandemic worldwide. The COVID-19 respiratory infection in humans is due to virus multiplication and causes severe respiratory tract complications. It is a single-stranded RNA virus and recognized as SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus and more commonly it is known as COVID-19 virus or 2019-nCoV [1,2]. The structural features of viruses have been explored including therapeutic targets protease, peptidase, spike protein ACE2 receptor s which has accelerated drug designing or discovery that can be used to manage the disease. Many natural compounds against these targets have been screened by computational biologist and it is suggested to conduct the further in vitro and in vivo evaluation against the virus targets [3,4,5]
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